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jonbrenasjonbrenas
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Merge branch 'master' into 583-GWSS-colors
2 parents b25acb2 + e3166e8 commit af6bac1

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4 files changed

+37
-1
lines changed

4 files changed

+37
-1
lines changed

‎malariagen_data/ag3.py‎

Lines changed: 5 additions & 1 deletion
Original file line numberDiff line numberDiff line change
@@ -378,6 +378,7 @@ def karyotype(
378378
inversion: inversion_param,
379379
sample_sets: Optional[base_params.sample_sets] = None,
380380
sample_query: Optional[base_params.sample_query] = None,
381+
sample_query_options: Optional[base_params.sample_query_options] = None,
381382
) -> pd.DataFrame:
382383
# load tag snp data
383384
df_tagsnps = self.load_inversion_tags(inversion=inversion)
@@ -390,7 +391,10 @@ def karyotype(
390391
region = f"{contig}:{start}-{end}"
391392

392393
ds_snps = self.snp_calls(
393-
region=region, sample_sets=sample_sets, sample_query=sample_query
394+
region=region,
395+
sample_sets=sample_sets,
396+
sample_query=sample_query,
397+
sample_query_options=sample_query_options,
394398
)
395399

396400
with self._spinner("Inferring karyotype from tag SNPs"):

‎malariagen_data/anoph/fst.py‎

Lines changed: 13 additions & 0 deletions
Original file line numberDiff line numberDiff line change
@@ -28,11 +28,13 @@ def __init__(
2828

2929
def _fst_gwss(
3030
self,
31+
*,
3132
contig,
3233
window_size,
3334
sample_sets,
3435
cohort1_query,
3536
cohort2_query,
37+
sample_query_options,
3638
site_mask,
3739
cohort_size,
3840
min_cohort_size,
@@ -46,6 +48,7 @@ def _fst_gwss(
4648
ac1 = self.snp_allele_counts(
4749
region=contig,
4850
sample_query=cohort1_query,
51+
sample_query_options=sample_query_options,
4952
sample_sets=sample_sets,
5053
site_mask=site_mask,
5154
cohort_size=cohort_size,
@@ -58,6 +61,7 @@ def _fst_gwss(
5861
ac2 = self.snp_allele_counts(
5962
region=contig,
6063
sample_query=cohort2_query,
64+
sample_query_options=sample_query_options,
6165
sample_sets=sample_sets,
6266
site_mask=site_mask,
6367
cohort_size=cohort_size,
@@ -104,6 +108,7 @@ def fst_gwss(
104108
window_size: fst_params.window_size,
105109
cohort1_query: base_params.sample_query,
106110
cohort2_query: base_params.sample_query,
111+
sample_query_options: Optional[base_params.sample_query_options] = None,
107112
sample_sets: Optional[base_params.sample_sets] = None,
108113
site_mask: Optional[base_params.site_mask] = base_params.DEFAULT,
109114
cohort_size: Optional[base_params.cohort_size] = fst_params.cohort_size_default,
@@ -127,6 +132,7 @@ def fst_gwss(
127132
window_size=window_size,
128133
cohort1_query=cohort1_query,
129134
cohort2_query=cohort2_query,
135+
sample_query_options=sample_query_options,
130136
sample_sets=self._prep_sample_sets_param(sample_sets=sample_sets),
131137
site_mask=self._prep_optional_site_mask_param(site_mask=site_mask),
132138
cohort_size=cohort_size,
@@ -161,6 +167,7 @@ def plot_fst_gwss_track(
161167
window_size: fst_params.window_size,
162168
cohort1_query: base_params.sample_query,
163169
cohort2_query: base_params.sample_query,
170+
sample_query_options: Optional[base_params.sample_query_options] = None,
164171
sample_sets: Optional[base_params.sample_sets] = None,
165172
site_mask: Optional[base_params.site_mask] = base_params.DEFAULT,
166173
cohort_size: Optional[base_params.cohort_size] = fst_params.cohort_size_default,
@@ -189,6 +196,7 @@ def plot_fst_gwss_track(
189196
max_cohort_size=max_cohort_size,
190197
cohort1_query=cohort1_query,
191198
cohort2_query=cohort2_query,
199+
sample_query_options=sample_query_options,
192200
sample_sets=sample_sets,
193201
site_mask=site_mask,
194202
random_seed=random_seed,
@@ -265,6 +273,7 @@ def plot_fst_gwss(
265273
window_size: fst_params.window_size,
266274
cohort1_query: base_params.sample_query,
267275
cohort2_query: base_params.sample_query,
276+
sample_query_options: Optional[base_params.sample_query_options] = None,
268277
sample_sets: Optional[base_params.sample_sets] = None,
269278
site_mask: Optional[base_params.site_mask] = base_params.DEFAULT,
270279
cohort_size: Optional[base_params.cohort_size] = fst_params.cohort_size_default,
@@ -290,6 +299,7 @@ def plot_fst_gwss(
290299
window_size=window_size,
291300
cohort1_query=cohort1_query,
292301
cohort2_query=cohort2_query,
302+
sample_query_options=sample_query_options,
293303
sample_sets=sample_sets,
294304
site_mask=site_mask,
295305
cohort_size=cohort_size,
@@ -348,6 +358,7 @@ def average_fst(
348358
region: base_params.region,
349359
cohort1_query: base_params.sample_query,
350360
cohort2_query: base_params.sample_query,
361+
sample_query_options: Optional[base_params.sample_query] = None,
351362
sample_sets: Optional[base_params.sample_sets] = None,
352363
cohort_size: Optional[base_params.cohort_size] = fst_params.cohort_size_default,
353364
min_cohort_size: Optional[
@@ -366,6 +377,7 @@ def average_fst(
366377
region=region,
367378
sample_sets=sample_sets,
368379
sample_query=cohort1_query,
380+
sample_query_options=sample_query_options,
369381
cohort_size=cohort_size,
370382
site_mask=site_mask,
371383
site_class=site_class,
@@ -377,6 +389,7 @@ def average_fst(
377389
region=region,
378390
sample_sets=sample_sets,
379391
sample_query=cohort2_query,
392+
sample_query_options=sample_query_options,
380393
cohort_size=cohort_size,
381394
site_mask=site_mask,
382395
site_class=site_class,

‎malariagen_data/anoph/h1x.py‎

Lines changed: 10 additions & 0 deletions
Original file line numberDiff line numberDiff line change
@@ -26,12 +26,14 @@ def __init__(
2626

2727
def _h1x_gwss(
2828
self,
29+
*,
2930
contig,
3031
analysis,
3132
window_size,
3233
sample_sets,
3334
cohort1_query,
3435
cohort2_query,
36+
sample_query_options,
3537
cohort_size,
3638
min_cohort_size,
3739
max_cohort_size,
@@ -44,6 +46,7 @@ def _h1x_gwss(
4446
region=contig,
4547
analysis=analysis,
4648
sample_query=cohort1_query,
49+
sample_query_options=sample_query_options,
4750
sample_sets=sample_sets,
4851
cohort_size=cohort_size,
4952
min_cohort_size=min_cohort_size,
@@ -56,6 +59,7 @@ def _h1x_gwss(
5659
region=contig,
5760
analysis=analysis,
5861
sample_query=cohort2_query,
62+
sample_query_options=sample_query_options,
5963
sample_sets=sample_sets,
6064
cohort_size=cohort_size,
6165
min_cohort_size=min_cohort_size,
@@ -111,6 +115,7 @@ def h1x_gwss(
111115
window_size: h12_params.window_size,
112116
cohort1_query: base_params.sample_query,
113117
cohort2_query: base_params.sample_query,
118+
sample_query_options: Optional[base_params.sample_query_options] = None,
114119
analysis: hap_params.analysis = base_params.DEFAULT,
115120
sample_sets: Optional[base_params.sample_sets] = None,
116121
cohort_size: Optional[base_params.cohort_size] = h12_params.cohort_size_default,
@@ -137,6 +142,7 @@ def h1x_gwss(
137142
# are different in the haplotype data.
138143
cohort1_query=cohort1_query,
139144
cohort2_query=cohort2_query,
145+
sample_query_options=sample_query_options,
140146
sample_sets=self._prep_sample_sets_param(sample_sets=sample_sets),
141147
cohort_size=cohort_size,
142148
min_cohort_size=min_cohort_size,
@@ -170,6 +176,7 @@ def plot_h1x_gwss_track(
170176
window_size: h12_params.window_size,
171177
cohort1_query: base_params.cohort1_query,
172178
cohort2_query: base_params.cohort2_query,
179+
sample_query_options: Optional[base_params.sample_query_options] = None,
173180
analysis: hap_params.analysis = base_params.DEFAULT,
174181
sample_sets: Optional[base_params.sample_sets] = None,
175182
cohort_size: Optional[base_params.cohort_size] = h12_params.cohort_size_default,
@@ -201,6 +208,7 @@ def plot_h1x_gwss_track(
201208
max_cohort_size=max_cohort_size,
202209
cohort1_query=cohort1_query,
203210
cohort2_query=cohort2_query,
211+
sample_query_options=sample_query_options,
204212
sample_sets=sample_sets,
205213
random_seed=random_seed,
206214
chunks=chunks,
@@ -276,6 +284,7 @@ def plot_h1x_gwss(
276284
window_size: h12_params.window_size,
277285
cohort1_query: base_params.cohort1_query,
278286
cohort2_query: base_params.cohort2_query,
287+
sample_query_options: Optional[base_params.sample_query_options] = None,
279288
analysis: hap_params.analysis = base_params.DEFAULT,
280289
sample_sets: Optional[base_params.sample_sets] = None,
281290
cohort_size: Optional[base_params.cohort_size] = h12_params.cohort_size_default,
@@ -304,6 +313,7 @@ def plot_h1x_gwss(
304313
window_size=window_size,
305314
cohort1_query=cohort1_query,
306315
cohort2_query=cohort2_query,
316+
sample_query_options=sample_query_options,
307317
sample_sets=sample_sets,
308318
cohort_size=cohort_size,
309319
min_cohort_size=min_cohort_size,

‎malariagen_data/anopheles.py‎

Lines changed: 9 additions & 0 deletions
Original file line numberDiff line numberDiff line change
@@ -2253,6 +2253,7 @@ def plot_xpehh_gwss(
22532253
sample_sets: Optional[base_params.sample_sets] = None,
22542254
cohort1_query: Optional[base_params.sample_query] = None,
22552255
cohort2_query: Optional[base_params.sample_query] = None,
2256+
sample_query_options: Optional[base_params.sample_query_options] = None,
22562257
window_size: xpehh_params.window_size = xpehh_params.window_size_default,
22572258
percentiles: xpehh_params.percentiles = xpehh_params.percentiles_default,
22582259
filter_min_maf: xpehh_params.filter_min_maf = xpehh_params.filter_min_maf_default,
@@ -2287,6 +2288,7 @@ def plot_xpehh_gwss(
22872288
sample_sets=sample_sets,
22882289
cohort1_query=cohort1_query,
22892290
cohort2_query=cohort2_query,
2291+
sample_query_options=sample_query_options,
22902292
window_size=window_size,
22912293
percentiles=percentiles,
22922294
palette=palette,
@@ -2457,6 +2459,7 @@ def xpehh_gwss(
24572459
sample_sets: Optional[base_params.sample_sets] = None,
24582460
cohort1_query: Optional[base_params.sample_query] = None,
24592461
cohort2_query: Optional[base_params.sample_query] = None,
2462+
sample_query_options: Optional[base_params.sample_query_options] = None,
24602463
window_size: xpehh_params.window_size = xpehh_params.window_size_default,
24612464
percentiles: xpehh_params.percentiles = xpehh_params.percentiles_default,
24622465
filter_min_maf: xpehh_params.filter_min_maf = xpehh_params.filter_min_maf_default,
@@ -2498,6 +2501,7 @@ def xpehh_gwss(
24982501
# are different in the haplotype data.
24992502
cohort1_query=cohort1_query,
25002503
cohort2_query=cohort2_query,
2504+
sample_query_options=sample_query_options,
25012505
min_cohort_size=min_cohort_size,
25022506
max_cohort_size=max_cohort_size,
25032507
random_seed=random_seed,
@@ -2525,6 +2529,7 @@ def _xpehh_gwss(
25252529
sample_sets,
25262530
cohort1_query,
25272531
cohort2_query,
2532+
sample_query_options,
25282533
window_size,
25292534
percentiles,
25302535
filter_min_maf,
@@ -2544,6 +2549,7 @@ def _xpehh_gwss(
25442549
region=contig,
25452550
analysis=analysis,
25462551
sample_query=cohort1_query,
2552+
sample_query_options=sample_query_options,
25472553
sample_sets=sample_sets,
25482554
min_cohort_size=min_cohort_size,
25492555
max_cohort_size=max_cohort_size,
@@ -2556,6 +2562,7 @@ def _xpehh_gwss(
25562562
region=contig,
25572563
analysis=analysis,
25582564
sample_query=cohort2_query,
2565+
sample_query_options=sample_query_options,
25592566
sample_sets=sample_sets,
25602567
min_cohort_size=min_cohort_size,
25612568
max_cohort_size=max_cohort_size,
@@ -2628,6 +2635,7 @@ def plot_xpehh_gwss_track(
26282635
sample_sets: Optional[base_params.sample_sets] = None,
26292636
cohort1_query: Optional[base_params.sample_query] = None,
26302637
cohort2_query: Optional[base_params.sample_query] = None,
2638+
sample_query_options: Optional[base_params.sample_query_options] = None,
26312639
window_size: xpehh_params.window_size = xpehh_params.window_size_default,
26322640
percentiles: xpehh_params.percentiles = xpehh_params.percentiles_default,
26332641
filter_min_maf: xpehh_params.filter_min_maf = xpehh_params.filter_min_maf_default,
@@ -2672,6 +2680,7 @@ def plot_xpehh_gwss_track(
26722680
max_cohort_size=max_cohort_size,
26732681
cohort1_query=cohort1_query,
26742682
cohort2_query=cohort2_query,
2683+
sample_query_options=sample_query_options,
26752684
sample_sets=sample_sets,
26762685
random_seed=random_seed,
26772686
chunks=chunks,

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